What is a species?

  • No one really knows

Physical barriers lead to isolation

Currents and islands as geographic barriers in the Indonesian Islands

  • Isolation eventually leads to speciation

Eviota atriventris

  • the Blackbelly dwarf goby
  • a cryptobenthic reef fish

Plot twist

  • some E. atriventris don't have a black belly

Are they different?

  • examine external morphology

Pelvic fin morphology data

  • contains individual ID no, sample locality, region (east or west), sex, pelvic fin characters
##    Specimen DNA. X         locality haplotype SL.mm.    sex
## 1 ROM 92305   no   Papua New Guinea      east   17.9   male
## 2 ROM 92305   no   Papua New Guinea      east   14.5   male
## 3 ROM 92305   no   Papua New Guinea      east   14.3   male
## 4 ROM 92309   no   Papua New Guinea      east   16.2 female
## 5 ROM 92309   no   Papua New Guinea      east   17.6   male
## 6 ROM 84482   no              Palau      west   17.9   male
##   fifth_fourth_ratio pelvic_length membrane_length branches
## 1               0.79           3.5            0.75        2
## 2               0.50           4.0            0.75        2
## 3               0.50            NA            0.75       NA
## 4               0.50           3.5            0.75        2
## 5                 NA            NA              NA       NA
## 6               0.50           4.1            0.50        6
##                         jaw_eye
## 1      anterior margin of pupil
## 2      anterior margin of pupil
## 3      anterior margin of pupil
## 4               middle of pupil
## 5               middle of pupil
## 6 middle of pupil (see picture)

Cleaning up data

  • I only actually need a few of these columns
morph_better = morph %>%
  dplyr::select(locality, haplotype, fifth_fourth_ratio, pelvic_length, membrane_length)
locality haplotype fifth_fourth_ratio pelvic_length membrane_length
Papua New Guinea east 0.79 3.5 0.75
Papua New Guinea east 0.50 4.0 0.75
Papua New Guinea east 0.50 NA 0.75
Papua New Guinea east 0.50 3.5 0.75
Papua New Guinea east NA NA NA
Palau west 0.50 4.1 0.50

Comparing branch number between eastern and western populations

-shows no difference between eastern and western morphs

Analyzing all four pelvic characters at once

  • we will use a principal component analysis
## 
## Loadings:
##                    Comp.1 Comp.2 Comp.3 Comp.4
## fifth_fourth_ratio  0.558 -0.159  0.738  0.346
## pelvic_ratio       -0.556  0.219  0.672 -0.437
## fin_membrane        0.596  0.102        -0.794
## branches           -0.157 -0.957        -0.242
## 
##                Comp.1 Comp.2 Comp.3 Comp.4
## SS loadings      1.00   1.00   1.00   1.00
## Proportion Var   0.25   0.25   0.25   0.25
## Cumulative Var   0.25   0.50   0.75   1.00

PCA Plot

Synthesis

  • it is interesting that there is no morphological difference
  • but there are genetic differences